Potential Gaps in catabolism of small carbon sources in Phyllobacterium brassicacearum STM 196
Found 38 low-confidence and 41 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | CU102_RS19315 | CU102_RS18560 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | CU102_RS05090 | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CU102_RS21775 | CU102_RS07510 |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | CU102_RS21800 | CU102_RS23515 |
| alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | CU102_RS21785 | CU102_RS23530 |
| arabinose | xacD: L-arabinonate dehydratase | CU102_RS23445 | CU102_RS18375 |
| arabinose | xacF: alpha-ketoglutarate semialdehyde dehydrogenase | CU102_RS05845 | CU102_RS19905 |
| cellobiose | cbp: cellobiose phosphorylase | CU102_RS17285 | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | CU102_RS13425 | CU102_RS11805 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CU102_RS07735 | CU102_RS27300 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CU102_RS07750 | CU102_RS05665 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CU102_RS07745 | CU102_RS05660 |
| citrulline | arcC: carbamate kinase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | CU102_RS20650 | CU102_RS20885 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CU102_RS18370 | CU102_RS17075 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | CU102_RS27940 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| galactose | dgoD: D-galactonate dehydratase | CU102_RS23445 | CU102_RS18375 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | CU102_RS23320 | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | CU102_RS23350 | |
| gluconate | gntA: gluconate TRAP transporter, small permease component | CU102_RS25485 | |
| gluconate | gntB: gluconate TRAP transporter, large permease component | CU102_RS25480 | CU102_RS17555 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxaC: D-glucuronate isomerase | CU102_RS23350 | |
| lactose | dgoD: D-galactonate dehydratase | CU102_RS23445 | CU102_RS18375 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | CU102_RS13700 | CU102_RS18480 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | CU102_RS27085 | CU102_RS16040 |
| lysine | lysN: 2-aminoadipate transaminase | CU102_RS03165 | CU102_RS07230 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | CU102_RS01195 | CU102_RS07670 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | CU102_RS17065 | CU102_RS19475 |
| mannose | man-isomerase: D-mannose isomerase | | |
| phenylacetate | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | | |
| phenylacetate | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | | |
| phenylacetate | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | | |
| phenylacetate | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | CU102_RS13700 | CU102_RS18480 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CU102_RS13700 | CU102_RS18480 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | CU102_RS14135 | CU102_RS10355 |
| phenylacetate | paaK: phenylacetate-CoA ligase | CU102_RS02485 | CU102_RS20310 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CU102_RS13700 | CU102_RS16670 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | CU102_RS26750 | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | CU102_RS21800 | CU102_RS20135 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | CU102_RS21775 | CU102_RS07510 |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | CU102_RS11390 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | put1: proline dehydrogenase | CU102_RS07620 | CU102_RS18830 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | CU102_RS02250 | CU102_RS09555 |
| ribose | rbsK: ribokinase | CU102_RS00810 | CU102_RS02690 |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CU102_RS21775 | CU102_RS07510 |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | CU102_RS21800 | CU102_RS23515 |
| serine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | CU102_RS21785 | CU102_RS23530 |
| sucrose | SUS: sucrose synthase | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CU102_RS21775 | CU102_RS07510 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | CU102_RS21800 | CU102_RS23515 |
| threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | CU102_RS21785 | CU102_RS23530 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | PsTP: trehalose phosphorylase | | |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | CU102_RS05110 | CU102_RS07830 |
| tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | CU102_RS05105 | |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | CU102_RS05100 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | kynB: kynurenine formamidase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | CU102_RS06015 | CU102_RS00185 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CU102_RS21825 | CU102_RS07710 |
| xylitol | PS417_12055: xylitol ABC transporter, substrate-binding component | CU102_RS28790 | CU102_RS19525 |
| xylitol | PS417_12065: xylitol ABC transporter, ATPase component | CU102_RS28785 | CU102_RS25570 |
| xylitol | xdhA: xylitol dehydrogenase | CU102_RS17560 | CU102_RS23605 |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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About GapMind
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using
ublast (a fast alternative to protein BLAST)
against a database of manually-curated proteins (most of which are experimentally characterized) or by using
HMMer with enzyme models (usually from
TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps."
For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways.
For diverse bacteria and archaea that can utilize a carbon source, there is a complete
high-confidence catabolic pathway (including a transporter) just 38% of the time, and
there is a complete medium-confidence pathway 63% of the time.
Gaps may be due to:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory